TnSeqCorr

• These are correlations of TnSeq responses across 82 experimental conditions.
• LFCs (log2-fold-changes) were computed for each gene in each condition relative to a relevant control condition (e.g. H37Rv grown on 7H9).
• The LFCs were normalized by dividing by the standard deviation for each condition. (so roughly, |LFC|>2 are the outliers, i.e. tails of the distribution)
• Note that essential genes often have LFCs around 0.
• Data for some genes is not available if they have less than 3 TA sites, or the dynamic range of LFCs is less than 2.0 across all conditions. (This is the case for many essential genes.)
• 'leverage' on each plot is a statistical score that indicates how much the regression is influenced by a few outlier points; the traditional threshold is indicated on the plots (3p/n, which is about 0.07 for this dataset), but in practice, cases with leverage > ~0.2 seem to be the least reliable (most misleading) correlation coefficients.

Top 10 genes with highest correlation to Rv3770B/-:

update plot	correlation	link to info on gene
Rv1831/-	(cc=0.5911)	info on Rv1831/-
Rv0222/echA1	(cc=0.5824)	info on Rv0222/echA1
Rv1616/-	(cc=0.5693)	info on Rv1616/-
Rv3146/nuoB	(cc=0.5674)	info on Rv3146/nuoB
Rv0309/-	(cc=0.5335)	info on Rv0309/-
Rv1505c/-	(cc=0.5273)	info on Rv1505c/-
Rv2825c/-	(cc=0.5243)	info on Rv2825c/-
Rv2495c/bkdC	(cc=0.5208)	info on Rv2495c/bkdC
Rv2456c/-	(cc=0.5148)	info on Rv2456c/-
Rv3470c/ilvB2	(cc=0.514)	info on Rv3470c/ilvB2

Correlation of Rv3770B/- with Rv1505c/-

Normalized LFCs for Rv3770B/-:
(description and provenance of datasets)

	Rv3770B/-	Rv1505c/-
Fe_supp_jason_reseq	-1.675	0.398
low_pH_jason_reseq	-1.302	-0.35
NO_jason_reseq	-0.16	0.247
B6_jason_reseq	-2.219	-1.795
MHCII_jason_reseq	-3.504	-1.356
Isoniazid02	0.819	1.695
Rifampicin4	-0.842	-0.244
Ethambutol3	0.026	0.896
Meropenem3	-0.31	-0.284
Vancomycin16	1.173	0.0
Rv2680_day32	0.368	-0.332
H37Rv_KO_MarP	-0.346	-0.579
hypoxia_3wks	-0.211	-0.144
hypoxia_6wks	-0.342	0.0
glycerol	1.542	-0.396
cholesterol	2.008	-0.847
AJ	0.18	-0.071
Bibs02	-0.319	0.604
Bibs02c	0.681	-0.567
BL6	2.153	1.544
BL6a	2.365	1.908
BXD01	1.88	1.315
BXD010	1.015	1.351
BXD011	1.725	1.424
BXD03	1.77	1.73
BXD04	3.099	1.686
BXD05	2.054	1.878
BXD06	2.271	2.076
BXD07	2.047	1.562
BXD08	2.3	1.373
BXD09	2.524	2.422
CAST	2.865	0.709
CCcont	1.557	1.366
DS01	-1.619	0.204
DS02	0.128	-1.511
DS04	2.781	0.641
DS0c	1.114	-0.506
GP01	1.543	0.539
GP02	-1.205	0.938
GP0c	0.404	0.511
NOD	2.257	2.294
NZO	-1.793	-0.786
PWK	1.361	0.274
H37Rv_KO_CtpC	-0.033	1.294
H37Rv_KO_CtpD	0.121	2.274
H37Rv_KO_Rv1272	0.918	1.29
H37Rv_KO_SugABC	1.782	-0.748
H37Rv_KO_MbtN	2.066	1.363
Trans05	2.42	1.179
macrophage_unactivated	0.331	0.167
IL1	0.211	0.489
Rapamycin	0.028	0.203
Tcell	1.219	0.73
GMCSF	-0.145	-0.219
IFNab	1.533	0.16
IFNg	0.457	-0.072
IFNg_GMCSF1	1.389	0.167
Rv1432_day32	0.0	0.288
Rv1565c_day32	1.204	-0.292
secA2_input	-0.266	-1.018
delta_Rv3594	1.747	0.197
delta_Rv3717	0.292	-0.56
delta_Rv3811	0.836	0.223
delta_Rv0954	-0.942	0.656
PonA1	1.377	-0.164
EccD1_KO	0.664	0.059
EspI_KO	0.693	-0.163
PE35_KO	0.825	-0.055
PPE68_KO	-0.358	-0.368
glycerol2	0.464	-0.488
lignocerate	-0.884	-0.477
oleate	0.224	-0.432
phosphatidylcholine	0.231	-0.098
acetate	-1.584	-0.848
glucAc	-2.417	-1.106
Rv0950ko	1.098	0.6
Rv1096ko	1.794	-0.525
Rv3684ko	1.677	0.311
delta_otsA_trehalose	-2.395	1.395